Open Access Highly Accessed Research article

Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions

Sota Fujii12, Takushi Toda1, Shunsuke Kikuchi3, Ryutaro Suzuki3, Koji Yokoyama3, Hiroko Tsuchida3, Kentaro Yano3 and Kinya Toriyama1*

Author Affiliations

1 Laboratory of Environmental Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan

2 Graduate School of Science, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan

3 School of Agriculture, Meiji University, Kawasaki 214-8571, Japan

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BMC Genomics 2011, 12:279  doi:10.1186/1471-2164-12-279

Published: 1 June 2011

Additional files

Additional file 1:

Summary of mitochondrial genome size of different species. Values on vertical scale are the number of base pairs in each organelle. For metazoans, the average mitochondrial genome size of 1104 species is presented. Chloroplast genome size of Cucumis melo is unknown; however, given the constant chloroplast size in angiosperms it is estimated at around 150-160 kb.

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Additional file 2:

Northern blot analysis of orf181 and orf490 in calli (C) and seedlings (S). RNA expression was undetectable in orf490 or orf181, the two genes used as untranscribed background region. Hybridization signal of nad4 is shown as the positive control.

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Additional file 3:

Summary of inter-genic ORF (iORF) expression. Values are given as the mean of all probes within each iORF region.

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Additional file 4:

RT-PCR analysis of genes 10 iORFs and eight ncRNAs. RT-PCR analysis was performed using RNA isolated from calli, etiolated seedlings and green seedlings. rrn18, 18 S ribosomal RNA.

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Additional file 5:

Multiple alignment of deduced amino acid sequences of iORF_487 and iORF_502 with known transposable elements. Upper, alignment of iORF_487 with retroviral aspartyl protease domain of Arabidopsis thaliana Athila transposable element (AC022456_8). Lower, alignment of iORF_502 with part of reverse transcriptase domain of Phyllostachys edulis (ADB85398.1).

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Additional file 6:

Spreadsheet information of primers used for RT-PCR analysis. TU, name of the transcriptional unit; Start, start position of TU; End, end position of TU; Primer 1 and Primer 2, sequence information of primer pair sequences used for RT-PCR analysis.

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